8pnl

;Outward-open conformation of a Major Facilitator Superfamily (MFS) transporter MHAS2168, a homologue of Rv1410 from M. tuberculosis, in complex with an alpaca nanobody ;

Method: X-RAY DIFFRACTION D_max: 140.5 Å Quality: REASONABLE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8pnl
沉积日期 deposition_date	2023-06-30
结构标题 title	;Outward-open conformation of a Major Facilitator Superfamily (MFS) transporter MHAS2168, a homologue of Rv1410 from M. tuberculosis, in complex with an alpaca nanobody ;
关键词 keywords	Major Facilitator Superfamily transporter, Nanobody, Outward-open conformation, Triacylglyceride extraction, TRANSPORT PROTEIN; TRANSPORT PROTEIN
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	38.75 Å
回转半径 Rg (电子) rg_electron	38.08 Å
零角强度 I(0) i0	205263000.00
分子量 molecular_weight	124970.0 kDa
排除体积 excluded_volume	160620 Å³
包络体积 envelope_volume	207260 Å³
水化壳体积 shell_volume	47801 Å³
包络直径 envelope_diameter	153.1 Å
壳层 Rg shell_rg	41.43 Å
包络 Rg envelope_rg	38.02 Å
形状 Rg shape_rg	38.08 Å
总 Rg total_rg	38.33 Å
总原子数 total_atoms	18026
残基数 n_residues	1190
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	140.5 Å
Rg (实空间) rg_real	39.06 Å
Rg 误差 (实空间) rg_real_error	1.46 Å
I(0) (实空间) i0_real	2.0530e+08
I(0) 误差 (实空间) i0_real_error	3.4370e+06
Rg (倒空间) rg_reciprocal	38.87 Å
I(0) (倒空间) i0_reciprocal	205200000.0000
解质量估计 total_estimate	0.6355
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	48.0 Å
偏度 Skewness skewness	0.562
峰度 Kurtosis kurtosis	0.178
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	21650000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.725; Stabil: 1.000; Sysdev: 0.132; Positv: 1.000; Valcen: 0.904; Smooth: 0.782

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (2)

Entity 1 polymer

描述 description	Putative triacylglyceride transporter
分子量 formula_weight	57082.9 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C
原子数 atom_count	18026

MSAFPQTPNRLIRPRRTSRGIAISAGGLAVLLGALDTYVVVSIVTDIMRDVGIAVNQIQRVTPIITGYLLGYIAAMPLLGRASDRFGRKLLIQISLAGFALGSVITALATNLDVLVAGRVIQGAASGALLPVTLALAADLWATHKRAAVLGGVGAAQELGAVLGPIYGIFVVWLFHHWQAVFWVNVPLALIAMVLIHISLPPRVRTEEPQRVDVTGGLLLALALGLATIGLYNAEPDGKQVLPEYGPPLIIGAVIAAVAFLVWERFARTRLLDPAGVRFRPFLIALLVSLVTGGALMVTLVNVELFGQGVLGLDQDEAVFLLARFLIALPVGALLGGWIATRVGDRAVTAVGLLIAAGGFYLIAQWPADVLESRHDLGFVSLPTLDTDLAIAGFGLGLVIAPLTSAALRVVPAAQHGIASAAVVVARMIGMLIGIAALSAWGLYRFNQYLKEQLAALPPAPADFPGGQMAGQMMRLRTATVQAYVLQYGEIFAITAGLCVFGAVLGLFIAGRREHAEESADAVDGVSNARDRAPSAALEVLFQ

来源 Source

来源生物 organism	Mycolicibacterium hassiacum DSM 44199
NCBI 分类编号 ncbi_taxonomy_id	1122247
宿主生物 host_organism	Mycolicibacterium smegmatis MC2 155

Entity 2 polymer

描述 description	Nb_H2
分子量 formula_weight	13033.6 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D

GPSQGQLVESGGGLVQPGGSLRLSCADAGSIFNKFPMAWYRQAPGKERELVARISSGGSTNYADFVKGRFTISRDNAKSTLYLQMNSLKPEDTAMYYCARIINSASNIAYWGQGTRVTVSA

来源 Source

来源生物 organism	Vicugna pacos
NCBI 分类编号 ncbi_taxonomy_id	30538
宿主生物 host_organism	Escherichia coli MC1061

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7. 引用文献 (1)

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晶胞边长 a length_a	57.780 Å
晶胞边长 b length_b	160.700 Å
晶胞边长 c length_c	82.960 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	109.01 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	monoclinic

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	44.700 Å
R 因子 r_factor	0.2474
R_work r_work	0.2450
R_free r_free	0.2915

fit	/app/data/saxs_computation/pn/8pnl/8pnl.fit
pddf	/app/data/pr_computation/pn/8pnl/8pnl.pr.out
profile	/app/data/saxs_computation/pn/8pnl/8pnl.dat

;Outward-open conformation of a Major Facilitator Superfamily (MFS) transporter MHAS2168, a homologue of Rv1410 from M. tuberculosis, in complex with an alpaca nanobody ;

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)